What exact mainboard do you have? Some chipsets don't have enough
PCIe lanes for x16+x16 and will either do x16+x1 or x8+x8. Means If you
plug in an x16 card into the primary slot and a x4 card into the secondary slot,
then the mainboard will automatically choose x8+x8. If there's an x16 card
and a x1 card then the mainboard should switch to x16+x1 mode.
Many mainboards allow to set the mode in the BIOS, so you may like to
check. However, depending on you application, the performance increase
is probably very small.